Fig. 3: Natural co-infections detected between December 6, 2021 and February 27, 2022.

A Violin plot of main and secondary virus mutation ratios for the 21,387 samples, including 61 samples sequenced in duplicate. The lineage ratio is considered to be 0 in cases where less than 6 mutations were found or covered with at least 100x for any lineage. Positive secondary virus mutation ratios in independent duplicates with concordant virus identification were considered as potential co-infections and depicted with dots (n = 53). Colors indicate lineages: co-infections between Delta/BA.1 are in green, Delta/BA.2 in dark blue, and BA.1/BA.2 in salmon. B Correlation between the relative abundance of the minor lineage in n = 53 natural co-infections sequenced in duplicate. Relative abundance is measured by the median of allele frequencies specific to the minor lineage. Distributions of relative abundance in first and second replicates are depicted as marginal boxplots. Boxplot represents median and IQR, with upper and lower whiskers extending to the largest and smallest value, respectively. Dotted lines are drawn at 5%, which is the threshold used to call a mutation in the variant calling step of seqmet. Colors indicate lineage as in panel A. Shapes indicate whether the minor lineage is identified as the secondary or main lineage in duplicate or a potential discordance between duplicates. C Number of chimeric sequences detected among the 53 natural co-infections sequenced in duplicate, depending on the relative abundance of the minor lineage. Chimeric sequences were defined by sequences bearing specific mutations of two lineages, with a gradient of color depending on the number of specific mutations from the less abundant lineage: 0 mutation (light grey), 1–2 specific mutations (medium grey), >2 specific mutations (dark grey).